RNA editing is an important posttranscriptional process that alters the genetic information of RNA encoded by genomic DNA. Adenosine-to-inosine (A-to-I) editing is the most prevalent type of RNA editing in animal kingdom, catalyzed by adenosine deaminases acting on RNA (ADARs). Recently, genome-wide A-to-I RNA editing is discovered in fungi, involving adenosine deamination mechanisms distinct from animals. Aiming to draw more attention to RNA editing in fungi, here we discuss the considerations for deep sequencing data preparation and the available various methods for detecting RNA editing, with a special emphasis on their usability for fungal RNA editing detection. We describe computational protocols for the identification of candidate RNA editing sites in fungi by using two software packages REDItools and RES-Scanner with RNA sequencing (RNA-Seq) and genomic DNA sequencing (DNA-Seq) data.
Keywords: A-to-I editing; DNA-Seq; Inosine; RNA editing; RNA modifications; RNA-Seq.